There does not seem to be a way to "uncheck" a folder for multiple files at once on the "Mass Manage" menu. "Delete" while viewing in a folder deletes the physical file, and removes it from all folders. To "move" a group of files to a new folder, mass manage can now add them to an additional folder, but they all remain in the original folder also, and have to be selected and have the original folder "unchecked" one at a time.
Thanks for the request. I've made a note of this and put the request in for you.
Hope this helps,